** Run, in highly concentrated form (ie. 2 lanes, 1 sample of half of each purification for each lane), on two different PA gels.

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*** Stain one gel with Coomassie blue (protocol).

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*** Stain other with SYBR Gold (protocol).

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** Pray; post pics.

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==Week 1==

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<calendar>

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name=TChan/Notebook

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date=2006/5/01

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view=threemonths

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format=%name/%year-%month-%day

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weekstart=7

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</calendar>

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===F 6.16.06===

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====Relevant Papers Summaries====

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<biblio>

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rps1 pmid=8407909</biblio><br>

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Thrombin, a serine protease functioning in the blood clotting pathways, is bound by a DNA aptamer with the sequence GGTTGGTGTGGTTGG; this binding inactivates thrombin. Assays of the aptamer's binding site and specificity were done, showing that the aptamer binds thrombin over competitive analogues. Assays also showed that the aptamer binds thrombin subunit alpha-thrombin rather than gamma-thrombin, which is the active-site-containing part of thrombin - in other words, the aptamer doesn't change the functionality of the active site, but it does change the ability of the protein to bind its substrate in the necessary way for cleavage. The group pinpointed the binding activity to two specific lysine residues in the protein, Lys 21 and 65.

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<biblio>

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rps2 pmid=16493417</biblio><br>

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MscL and MscS are mechanosensitive ion channels, named for their respective large or small conductances. Their mechanosensitivity to lateral distension across the lipid bilayer They are in effect a 'last ditch response' to physical stress which might result in fatal osmolarity changes. MscL is a five subunit protein, each subunit being comprised of two transmembrane helices; MscS is also a five subunit protein, each subunit comprised of transmembrane helices with a one cytosolic section. MscL has a 2-angstrom diameter pore when closed, but MscS has been resolved with an 11-angstrom pore - whether this is true when MscS is in open or closed state has still to be determined, due to water dynamics studies showing that in this 11-angstrom wide state, the hydrophobic residues may from a "vapor lock," preventing any solubilized ion from passing through.

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===Th 6.15.06===

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1. RapidLigated 6uL of the insert (E0 fragments) and 1uL of the vector (R0 cut).